A New RING Finger Protein, PLANT ARCHITECTURE and GRAIN NUMBER 1, Affects Plant Architecture and Grain Yield in Rice

Yan, Peiwen; Yu, Zhao; Wang, Ying; Ma, Fuying; Lan, Dengyong; Niu, Fuan; Dong, Shiqi; Zhang, Xinwei; Hu, Jian; Liu, Siwen; Guo, Tao; Xin, Xiaoyun; Zhang, Shiyong; Yang, Jinshui; Cao, Liming; Luo, Xin

doi:10.3390/ijms23020824

Cited by 10 publications

(8 citation statements)

References 47 publications

(52 reference statements)

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“…The RING-type E3-ubiqitin-ligase barley genes ( HvYrg1–2 ) control the characteristics of both vegetative organs (leaf width and weight, plant weight and height, flowering-time, grain-filling duration, root-growth) and seed components (thousand-grain weight and seed morphology) in barley [ 65 ]. A novel RING finger protein, i.e., PLANT ARCHITECTURE and GRAIN NUMBER 1 (PAGN1 ) regulates the number of grains per panicle, the plant height, and the number of tillers in rice [ 66 ].…”

Section: Discussionmentioning

confidence: 99%

Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

Rathan

Krishnappa

Singh

et al. 2023

Plants

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Genomic regions governing days to heading (DH), days to maturity (DM), plant height (PH), thousand-kernel weight (TKW), and test weight (TW) were investigated in a set of 190 RILs derived from a cross between a widely cultivated wheat-variety, Kachu (DPW-621-50), and a high-zinc variety, Zinc-Shakti. The RIL population was genotyped using 909 DArTseq markers and phenotyped in three environments. The constructed genetic map had a total genetic length of 4665 cM, with an average marker density of 5.13 cM. A total of thirty-seven novel quantitative trait loci (QTL), including twelve for PH, six for DH, five for DM, eight for TKW and six for TW were identified. A set of 20 stable QTLs associated with the expression of DH, DM, PH, TKW, and TW were identified in two or more environments. Three novel pleiotropic genomic-regions harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the DArTseq markers were located on important putative candidate genes such as MLO-like protein, Phytochrome, Zinc finger and RING-type, Cytochrome P450 and pentatricopeptide repeat, involved in the regulation of pollen maturity, the photoperiodic modulation of flowering-time, abiotic-stress tolerance, grain-filling duration, thousand-kernel weight, seed morphology, and plant growth and development. The identified novel QTLs, particularly stable and co-localized QTLs, will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).

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Section: Discussionmentioning

confidence: 99%

Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

Rathan

Krishnappa

Singh

et al. 2023

Plants

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“…Interestingly, there are two candidates, LOC_Os02G17470 (RNA binding protein-related) and LOC_Os07G43870(DNA J heat shock protein) gene which act as a positive regulator of pollen and pollen tube growth which is essentially important for reproduction in plants [ 122 , 123 ]. Also, LOC_Os03G08000 (E3 ubiquitin ligase family protein), involved in proteolysis and regulation of developmental processes, has been found to be located near to the QTN, 83271479 associated with PYD and PlHt indicating a possible role in grain yield [ 9 , 124 , 125 ]. Interesting, yield related gene monohydrate reductase gene LOC_Os08G05770, was observed in neighbouring region of the QTN associated with DTF, signifying a possible pleotropic effect on all the grain yield related traits [ 38 , 126 – 128 ].…”

Section: Discussionmentioning

confidence: 99%

“…Rice is one of the major cereal crops that feeds over half of the human population and has been grown mainly in Asian countries for more than hundred decades [ 1 – 3 ]. Increasing yield potential has been a long-term objective in rice breeding and is imperative to overcome the global food crisis [ 4 – 9 ]. Rice yield is the most targeted complex trait that is a direct function of multiple factors including number and size of grains, productive tillers per plant, plant count per unit area, size of panicles and plant height [ 2 , 7 , 10 – 12 ] thus, the aforesaid component traits are prerequisite for achieving the desired yield in rice.…”

Section: Introductionmentioning

confidence: 99%

New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study

Sachdeva,

Singh,

Maurya

et al. 2024

BMC Plant Biol

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Background Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield. Results Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield. Conclusions Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties.

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“…Similarly, the bHLH ( basic helix-loop-helix ) transcription factor ( arahy.4C0G14 ) and WD40/YVTN repeat-like-containing domain ( arahy.SF2S3L ) genes were shown to play a significant role in controlling seed development ( Heang and Sassa, 2012 ; Hu et al., 2018 ). A RING finger protein ( arahy.GU2JPA ) family gene was also linked to levels of active cytokinins, which control plant architecture and grain number ( Yan et al., 2022 ). Furthermore, the chaperone protein dnaJ-related ( arahy.T0XEU7 ) gene, which acts as a molecular chaperone, performed crucial roles in the genesis and growth of plants, as well as in their responses to heat stress ( Fan et al., 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic mapping identified three hotspot genomic regions and candidate genes controlling heat tolerance-related traits in groundnut

et al. 2023

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Groundnut productivity and quality have been impeded by rising temperatures in semi-arid environments. Hence, understanding the effects and molecular mechanisms of heat stress tolerance will aid in tackling yield losses. In this context, a recombinant inbred line (RIL) population was developed and phenotyped for eight seasons at three locations for agronomic, phenological, and physiological traits under heat stress. A genetic map was constructed using genotyping-by-sequencing with 478 single-nucleotide polymorphism (SNP) loci spanning a map distance of 1,961.39 cM. Quantitative trait locus (QTL) analysis using phenotypic and genotypic data identified 45 major main-effect QTLs for 21 traits. Intriguingly, three QTL clusters (Cluster-1-Ah03, Cluster-2-Ah12, and Cluster-3-Ah20) harbor more than half of the major QTLs (30/45, 66.6%) for various heat tolerant traits, explaining 10.4%–38.6%, 10.6%–44.6%, and 10.1%–49.5% of phenotypic variance, respectively. Furthermore, important candidate genes encoding DHHC-type zinc finger family protein (arahy.J0Y6Y5), peptide transporter 1 (arahy.8ZMT0C), pentatricopeptide repeat-containing protein (arahy.4A4JE9), Ulp1 protease family (arahy.X568GS), Kelch repeat F-box protein (arahy.I7X4PC), FRIGIDA-like protein (arahy.0C3V8Z), and post-illumination chlorophyll fluorescence increase (arahy.92ZGJC) were the underlying three QTL clusters. The putative functions of these genes suggested their involvement in seed development, regulating plant architecture, yield, genesis and growth of plants, flowering time regulation, and photosynthesis. Our results could provide a platform for further fine mapping, gene discovery, and developing markers for genomics-assisted breeding to develop heat-tolerant groundnut varieties.

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A New RING Finger Protein, PLANT ARCHITECTURE and GRAIN NUMBER 1, Affects Plant Architecture and Grain Yield in Rice

Cited by 10 publications

References 47 publications

Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study

Genetic mapping identified three hotspot genomic regions and candidate genes controlling heat tolerance-related traits in groundnut

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